I'm sure it's been brought up before but... (Spoilers)

My understanding is, Elizabeth drowned all Bookers that accepted the baptism across all realities, thus making sure that Comstock can't come to be.

That, or Elizabeth just drowned Booker across all realities regardless of his decision to accept the baptism or not.

"Greetings! This is not God, but his close friend, Officer Boscorelli. Please pull over."- Bosco

If all Bookers across all realities were drowned, how would the ending after the credits make sense?

Or why would drowning a 40 year old Booker stop 20 year old Booker from becoming Comstock?

I was always under the impression that he was in the world where he would accept the baptism and become Comstock, hence Elizabeth saying "This isn't the same place" when Booker asks why they are back there.

Even if this isn't the case, the point of drowning Booker is that:
Booker can never exist to become Comstock which means Elizabeth cannot be stolen and gain powers to come back and kill him in the first place.

This would mean that the paradox is only created should Booker ever decide to take the baptism and become Comstock. So every world in which Booker accepts the baptism is removed because with every Comstock comes a paradox.

This means that the only timelines that can exist are the ones in which Booker denies the baptism, as they are the only ones where Anna can never be taken through to Comstock's reality and thus gaining powers.

With the existence of only the one decision, it also means that this Booker is never drowned by Elizabeth because she can no longer exist

Hence the after credit scene

Drowning Dewitt basically erases the bubble universe whereupon he became Comstock and funded Columbia. All that's left is the bigger universe where the notion of Comstock never existed.

Booker always has it in him to become Comstock, so the only way to ensure that there is no Comstock is to drown Booker in all realities.

Actually, you are absolutely correct, the ending does not make any sense - not if you actually put any thought into it. In the multiverse, there is always an alternative -

All in all, multiverse is nothing more but a plot device. The suggestion here is such that there is no multiverse - and that the multiverse we have seen in this game was created solely due to actions of booker where he was baptized in one world and opted not to in another world, which led to the creation of a thousand different worlds. The idea of booker being the sole creator of a multiverse is ludicrous - especially given that we did not observe him to be anything special - nor having any sort of divine powers.

If booker could have been the origin of multiverse, than it is equally possible for any other human being to be the origin of yet another thousand multiverses - but that would also mean that booker's actions would have little impact on worlds which are hinged on actions of other people.

The point being, it's a good plot device that is used very poorly in this game, and when you also combine this poorly thought out plot with standard fps gameplay, I believe that this game is probably the most overhyped game of the decade, much like batman films.